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Bowser is working to do some repairs to his castle with his contracter, Monty Mole. A ball flies into the room and hits Bowser on the head. and Bowser tells Monty to wait, while Ludwig and Morton are fighting. Ludwig gets upset that Morton threw his ball, and Morton says he did it because Ludwig got rid of his lucky dice. They start to fight again, when suddenly Bowser enters. He tells them to stop, and asks where Bowser Jr. is. Ludwig says something happened, and they ended up stuffing him in the hamper. Bowser Jr. pops out and says he breathed in a sock. Bowser Jr. is mad at his brothers, and starts to ambush Ludwig and Morton, until Bowser grabs Jr. and puts him down. Bowser explains that Iggy is in a mental asylum, Lemmy is being foster parented, and the rest of the Koopalings, as far as he knows, are still in the basement, with some rats, hunting for food. Bowser says he doesn't want Bowser Jr, Ludwig, and Morton to end up like them, so he enrolls them in a disciplinary school, much to the Koopalings' dismay.

Bowser is wandering around the town looking for the school. He opens a door, thinking it is the school, and he sees a disturbing scene with Waluigi scrubbing Wario's butt. Wario screams and tells Bowser to close the door. Bowser closes the door, still scarred from what he saw. Soon after, he finds Luigi (with sunglasses) in a dark alley. Luigi tells Bowser to give him the kids. Bowser, although confused by how shady the school looks, gives him the kids, and gives Luigi twenty dollars. They disappear into thin air, and Bowser, disturbed, walks off to continue the construction at his castle.

They get to the school, and Luigi introduces himself to the Koopalings, and orders them to take their seats immediately. Luigi tells Bowser Jr, Morton, and Ludwig about the day's lesson, and a pre test that they will be taking at the beginning of the day. They take the test, and give many sarcastic answers, giving them a failing grade. Luigi goes on with the lesson. Then they do a deminstration of the lesson. No one volunteers to help. So Luigi commands Ludwig and Morton to do the act. Jr. laughs at Morton and Ludwig, to Ludwig's dismay. Luigi gives an scenario, that Ludwig stole Morton's lolli-pop, and tells them to demonstrate what they would do. Morton just ends up beating up Ludwig. Luigi tells them to stop. when Morton stomps to Luigi. Morton, much bigger and stronger than Luigi, asks Luigi is there a problem with what he did. Luigi, nervous, says, through stutters, that he was too assertive. They walk away and Ludwig and Morton call each other idiots.

Luigi calls Bowser Jr. to do a test of holding in their anger. Luigi throws jelly beans at Bowser Jr. while saying "Are you mad yet?" Eventually, Jr, angry at Luigi, throws a rock at Luigi, giving him a black eye.

Luigi tells the naughty children that he brought a special guest speaker named Hank. Hank introduces himself to the kids very strangely, causing Ludwig to think he is weirder than Luigi. He tells the class to feast their eyes and look at the world around them. He says he sees himself as a good child, and the Koopalings as bad scum. Hank tells them he wants to change the world into a different, more fashionable world. Hank says he is a prime example of a perfect being. He makes a corny joke, saying he's a primate example. Once Hank leaves, Luigi says Hank should win a nobel peace prize.

Next, Luigi tells the kids to follow him into the "kindness chamber", actually a dark room. Once inside, the Koopalings get scared, until Bowser Jr finds a light. Luigi says that the whole school was a set up. He calls for Mario and they beat Ludwig, Morton and Junior up.

They end up in a hospital, with Bowser by their side. Bowser asks the kids what happened. They tell him that they got pranked, and beat up by Luigi. Bowser is shocked that it was even Luigi who ran the school, showing Bowser's extreme gullibility, Bowser tells them he got the perfect doctor, who unfortunately for the Koopalings, turns out to be Dr. Mario!